Bei den meisten Bakterien wird die Biofilmbildung durch das Botenmolekül c-di-GMP stimuliert. Durch die enzymatische Aktivität von c-di-GMP-synthetisierenden Diguanylatzyklasen/DGC und c-di-GMP-abbauenden Phosphodiesterasen/PDE wird der c-di-GMP-Gehalt als eine Antwort auf diverse Stress- und suboptimale Umweltbedingungen reguliert. Vor allem Gram-negative Bakterien haben multiple DGC/PDE. So besitzt Escherichia coli K-12 29 solche Proteine, darunter 12 DGC, 13 PDE sowie 4 degenerierte Proteine ohne enzymatische Funktion. Dieses komplexe c-di-GMP-Kontrollsystem reguliert die Produktion der extrazellulären Biofilmmatrix, die in E. coli während des Übergangs in die stationäre Wachstumsphase stattfindet. Das Ziel dieser Arbeit war es zu untersuchen, ob die 29 DGC/PDE von E. coli ein spezifisches Interaktom bilden, das DGC/PDE-Pärchen enthält. Durch umfangreiche Two-Hybrid-Untersuchungen konnte gezeigt werden, dass es ein solches Interaktom in der Biofilmregulationskaskade tatsächlich gibt, das allerdings nicht in Pärchen organisiert ist. Vielmehr wird die Biofilmbildung von einer Kerngruppe von Enzymen, welche multiple Interaktionen untereinander und mit anderen DGC/PDE aufweisen, kontrolliert. Die Funktionsweise der Kerngruppe von Enzymen könnte jedoch möglicherweise unter bestimmten Wachstumsbedingungen durch Interaktionen mit weiteren Proteinen moduliert werden. Die Dynamik des Interaktionsnetzwerks ermöglicht vermutlich eine rationelle Ressourcenverwaltung in den verschiedenen Zonen des Biofilms, was zum Aufbau der komplexen Matrixarchitektur beitragen könnte, und eine hohe Anpassungsfähigkeit der Bakterien und der von ihnen aufgebauten Biofilmstrukturen gewährleisten könnte. Insgesamt führt diese Arbeit aus einer systemischen Perspektive zu einem neuen Modell der lokalen Biofilmbildungsregulation durch den Botenstoff c-di-GMP und legt die Basis für weitere Untersuchungen der daran beteiligten Mechanismen einzelner GGDEF/EAL-Domäne-haltiger Proteine in E. coli. / The messenger molecule c-di-GMP stimulates the formation biofilms in most bacteria species. The enzymatic activities of the diguanylate cyclases/DGC and the phosphodiesterases/PDE adjust the c-di-GMP content in response to diverse stress and suboptimal environmental conditions. Above all, Gram-negative bacteria have multiple GGDEF/EAL domain proteins. Escherichia coli K-12 possesses 29 of such proteins: 12 DGCs, 13 PDEs and 4 so called degenerate proteins without any enzymatical function. Mainly, this complex c-di-GMP control system regulates the production of the extracellular biofilm matrix, which in E. coli takes place during the switch into the stationary growth phase. The main compounds of the matrix are amyloid curli-fibers and exoplysaccaride cellulose. The goal of this work was to investigate, whether the 29 DGC/PDE from E. coli develop a specific interactome containing additional DGC/PDE pairs. In a comprehensive two-hybrid study, it could be demonstrated that there is indeed a specific interactome in the biofilm formation cascade. However, this interactome does not contain additional DGC/PDE pairs. Mainly, the core group of enzymes, which have multiple interactions among each other and with other DGC/PDE, controls biofilm formation. Under certain growth conditions the mode of action of the core enzymes might be adjusted through the interaction with other proteins. Presumably, the dynamics of the interaction network allows managing the resources in the different biofilm zones efficiently, which could conribute to the complex organisation of the matrix architecture. Therefore, the rapid adaptation of bacteria and the formed biofilm structures could be better organized. Altogether, this work provides a new model for the local regulation of the biofilm formation by the secondary messenger c-di-GMP guided from a systemical perspective. Hereby, the basis for further investigations on regulation mechanisms of individual DGC/PDE was set. / Переход от подвижного и планктонообразного образа жизни к формированию биоплёнок является важной и интересной особенностью различных микроорганизмов. Кишечная палочка (Escherichia coli) представляет собой удобный модельный организм для изучения подобных трансформаций. У этой грамотрицательной бактерии образование биоплёнки обусловлено внутриклеточной аккумуляцией циклического дигуанилата (цикло-диГМФ). Известно, что активность ферментов, синтезирующих (дигуанилатциклазы/ДГЦ) и разлагающих (диэстеразы/ДЭ) эти сигнальные молекулы, меняется в ответ на стрессовые и субоптимальные раздражители. Кишечная палочка имеет 12 ДГЦ, 13 ДЭ и четыре дегенерированных протеина. Цель данной работы – изучить специфический, важный при формировании биоплёнки интерактом и выяснить, способны ли другие ДГЦ/ДЭ образовывать дополнительные ДГЦ/ДЕ модули и вносить свой вклад в формирование биоплёнки. В работе были изучены молекулярные взаимодействия, ответственные за формирование биоплёнок у кишечной палочки. Так, было доказано отсутствие в интерактоме дополнительных локальных ДГЦ/ДЕ модулей, участвующих при каскадных процессах регуляции роста биоплёнки. Установлено, что процесс формирования биоплёнки в большей степени контролируется основной группой ферментов, которые имеют множественные взаимодействия между собой и с другими ДГЦ/ДЭ. Вероятнее всего, такие взаимодействия способны модулировать работу основных ферментов при определенных условиях культивирования. Динамика подобной сети взаимодействий позволяет микроорганизмам целесообразно использовать свои клеточные ресурсы при образовании биоплёнок и вносит свой вклад в её сложную архитектуру, повышая тем самым приспособляемость бактерий и созданных ими сложных биоплёночных структур к внешним условиям. В целом, в данной работе предложена новая модель локальной регуляции образования биоплёнки с помощью сигнальной молекулы цикло-диГМФ и заложен фундамент для дальнейших исследований механизмов действия отдельных ДГЦ/ДЭ.

O feijão-comum (Phaseolus vulgaris) é atacado por uma gama de patógenos que afetam a produtividade das lavouras e a qualidade dos grãos. Dentre os patógenos de importância econômica para a cultura no Brasil, destaca-se o nematoide das galhas (Meloidogyne incognita). Embora haja relatos sobre a avaliação de cultivares na presença de M. incognita, as fontes de resistência tem se mostrado pouco efetivas. Por isso, pesquisas que possibilitem um melhor entendimento sobre a interação planta-nematoide são de extrema valia e devem nortear novas estratégias para o melhoramento do feijoeiro. Assim, no presente estudo, 18 cultivares de P. vulgaris foram avaliadas quanto à resistência a M. incognita raça 3, sendo que quatro comportaram-se como pouco suscetíveis, 11 como moderadamente suscetíveis e três altamente suscetíveis. A cultivar IPR Saracura mostrou menor grau de suscetibilidade e foi, então, usada na construção de 12 bibliotecas de RNAseq, visando à identificação dos genes envolvidos na reposta à infecção pelo nematoide. Foram adotados dois tratamentos, 4 e 10 DAI (dias após inoculação), compostos de plantas inoculadas e controles. Primeiramente, realizou-se o mapeamento dos transcritos de cada biblioteca, tomando como referência o genoma de P. vulgaris (G19833), o que resultou na identificação de 27.195 unigenes. Em seguida, foi realizada a quantificação da expressão dos transcritos mapeados e genes diferencialmente expressos foram identificados. No total, 191 genes do hospedeiro apresentaram expressão diferencial, considerando-se: i) o tratamento inoculado em relação ao controle; ii) a razão de expressão (Fold Change - FC) mínima absoluta igual a 4; iii) o nível de significância ? = 0,05. Do total, 120 genes foram identificados aos 4 DAI e 71 aos 10 DAI. As sequências mapeadas foram contrastadas àquelas dos bancos de dados NCBI e TAIR, usando a ferramenta BLASTx e, posteriormente, anotadas usando os softwares Blast2GO e MapMan. Detectou-se similaridade com genes codificadores de proteínas conhecidas para 90% (24.604/27.195) dos unigenes, sendo que 69% (16.991/24.604) deles foram anotados. Quanto à expressão diferencial, 98% (188/191) dos transcritos mostraram similaridade com proteínas conhecidas e 67% (127/188) puderam ser anotados. Os transcritos foram atribuídos a diferentes categorias funcionais putativas, predominando o termo ontológico \'processos metabólicos\', em ambas as plataformas. A anotação dos genes na plataforma MapMan mostrou abundância das categorias da via de resposta a estresse, com predominância de genes de defesa superexpressos aos 4 DAI e reprimidos aos 10 DAI. Por fim, 10 genes mostraram expressão diferencial tanto aos 4 como aos 10 DAI: sete deles foram estáveis, sendo superexpressos nas plantas inoculadas, e três apresentaram comportamentos opostos nos momentos avaliados. Ênfase foi dada a um gene que codifica uma \'probable inactive ADP-ribosyltransferase\' e a quatro genes de resposta a ferimento. / The common bean (Phaseolus vulgaris) is attacked by a range of pathogens, which affect crop yield and the quality of grains. Among the pathogens of economic significance to the crop in Brazil, the root-knot nematodes (Meloidogyne incognita) deserve attention. Though there are some reports on cultivar evaluation in presence of M. incognita, the resistance sources have not being effective. Therefore, it is of valuable importance research projects that could lead to a better understanding of plant-nematode interaction and to indicate new strategies for common bean breeding. In the present study, 18 cultivars of P. vulgaris were evaluated in regard to their resistance to M. incognita race 3; four were less susceptible, 11 moderately susceptible, and three were highly susceptible. \'IPR Saracura\' behaved as the less susceptible cultivar and then was selected for the construction of 12 RNAseq libraries, aiming at the identification of genes differentially expressed in response to nematode infection. Two treatments were adopted, 4 and 10 days after inoculation (DAI), each comprised of inoculated and control plants. Firstly, the transcripts were mapped to the reference genome of P. vulgaris (G19833), resulting in the identification of 27,195 unigenes. Then, the mapped transcript\'s expression was quantified and differentially expressed genes were identified. In total, 191 genes of the host plant showed differential expression taking into consideration: i) the inoculated treatments in relation to their control; ii) an absolute fold change (FC) >= 4; iii) a level of significance ? = 0,05. Of the total, 120 genes were detected at 4 DAI and 71 at 10 DAI. The mapped sequences were compared against those deposited in NCBI and TAIR databanks using BLASTx and subsequently annotated using Blast2GO and MapMan softwares. Similarity to known proteins was detected for 90% of the unigenes (24,604/27,195) and 69% (16,991/24,604) of them were annotated. Regarding assessing differential expression, 98% (188/191) of the transcripts showed similarity to known proteins and 67% (127/188) were annotated. Transcripts were attributed to different putative functional categories and the ontological term \'metabolic process\' was predominant within both platforms. Gene annotation within MapMan platform showed predominance of stress-related pathway categories, with prevalence of defense genes overexpressed at 4 DAI and repressed at 10 DAI. Finally, 10 genes showed differential expression at both 4 and 10 DAI: seven were stably overexpressed in the inoculated plants, and three showed an opposite behavior regarding the evaluation periods. Attention was given to a gene encoding a probable inactive ADP-ribosyltransferase and four genes related to wound response.

Molecular interactions lie at the heart of myriad biological processes. Knowledge of molecular recognition processes and the ability to model and predict interactions of any biological molecule to any chemical compound are the key for better understanding of cell functions and discovery of more efficacious medicines. This thesis presents contributions to the development of a novel chemo-bioinformatics approach called proteochemometrics; a general method for interaction space analysis of biological macromolecules and their ligands. In this work we explore proteochemometrics-based interaction models over broad groups of protein families, evaluate their validity and scope, and compare proteochemometrics to traditional modeling approaches. Through the proteochemometric analysis of large interaction data sets of multiple retroviral proteases from various viral species we investigate complex mechanisms of drug resistance in HIV-1 and discover general physicochemical determinants of substrate cleavage efficiency and binding in retroviral proteases. We further demonstrate how global proteochemometric models can be used for design of protease inhibitors with broad activity on drug-resistant viral mutants, for monitoring drug resistance mechanisms in the physicochemical sense and prediction of potential HIV-1 evolution trajectories. We provide novel insights into the complexity of HIV-1 protease specificity by constructing a generalized IF-THEN rule model based on bioinformatics analysis of the largest set of HIV-1 protease substrates and non-substrates. We discuss how proteochemometrics can be used to map recognition sites of entire protein families in great detail and demonstrate how it can incorporate target variability into drug discovery process. Finally, we assess the utility of the proteochemometric approach in evaluation of ADMET properties of drug candidates with a special focus on inhibition of cytochrome P450 enzymes and investigate application of the approach in the pharmacogenomics field.

The availability of new technologies supplied life scientists with large amounts of experimental data. The data sets are large not only in terms of the number of observations, but also in terms of the number of recorded features. One of the aims of modeling is to explain a given phenomenon in possibly the simplest way, hence the need for selection of suitable features. We extended a Monte Carlo-based approach to selecting statistically significant features with discovery of feature interdependencies and used it in modeling sequence-function relationships in proteins. Our approach led to compact and easy-to-interpret predictive models. First, we represented protein sequences in terms of their physicochemical properties. This was followed by our feature selection and discovery of feature interdependencies. Finally, predictive models based on e.g., decision trees or rough sets were constructed. We applied the method to model two important biological problems: 1) HIV-1 resistance to reverse transcriptase-targeted drugs and 2) post-translational modifications of proteins. In the case of HIV resistance, we were not only able to predict whether the mutated protein is resistant to a drug or not, but we also suggested some new, previously neglected, mutations that possibly contribute to drug resistance. For all these mutations we proposed probable molecular mechanisms of action using literature and 3D structure studies. In the case of predicting PTMs, we built high accuracy models of modifications. In comparison to other methods, we were able to resolve whether the closest neighborhood of a residue (the nanomer) is sufficient to determine its modification status. Importantly, the application of our method yields networks of interdependent physicochemical properties of amino acids that show how these properties collaborate in establishing a given modification. We believe that the presented methods will help researchers to analyze a large class of important biological problems and will guide them in their research.

The first part of the thesis describes a systematic function analysis that identified in vitro E2 partners for ten different HECT E3 ligase proteins. Using mass spectrometry, the linkage composition for the resulting autoubiquitylation products of a number of functional E2-HECT pairs was determined. HECT domains from different subfamilies catalyze the formation of very different types of Ub chains, largely independent of the E2 in the reaction. The second part of the thesis describes the characterization of the RAD6-interactome. Using affinity purification coupled with mass spectrometry, I identified a novel RAD6-interacting E3 ligase, KCMF1, which binds to a different surface on RAD6 than the other RAD6-associated E3 ligases. KCMF1 also recruits additional proteins to RAD6, and this new complex points to novel RAD6 functions. Interestingly, the RAD6A R11Q mutant polypeptide, found in X-linked mental retardation patients specifically loses the interaction with KCMF1, but not with other RAD6-associated E3 ligases.

The first part of the thesis describes a systematic function analysis that identified in vitro E2 partners for ten different HECT E3 ligase proteins. Using mass spectrometry, the linkage composition for the resulting autoubiquitylation products of a number of functional E2-HECT pairs was determined. HECT domains from different subfamilies catalyze the formation of very different types of Ub chains, largely independent of the E2 in the reaction. The second part of the thesis describes the characterization of the RAD6-interactome. Using affinity purification coupled with mass spectrometry, I identified a novel RAD6-interacting E3 ligase, KCMF1, which binds to a different surface on RAD6 than the other RAD6-associated E3 ligases. KCMF1 also recruits additional proteins to RAD6, and this new complex points to novel RAD6 functions. Interestingly, the RAD6A R11Q mutant polypeptide, found in X-linked mental retardation patients specifically loses the interaction with KCMF1, but not with other RAD6-associated E3 ligases.

Με την αλληλούχιση του ανθρώπινου γονιδιώματος αλλά και άλλων οργανισμών, μια νέα εποχή άρχισε για την επιστήμη της βιολογίας, γνωστή ως "μεταγονιδιωματική εποχή". Ο όρος σε καμιά περίπτωση δεν σηματοδοτεί το τέλος της αλληλούχισης ή της ανάλυσης των ήδη αλληλουχημένων γονιδιωμάτων, απλά δηλώνει πως οι τεχνικοί περιορισμοί για την ανίχνευση γονιδιωματικής πληροφορίας έχουν σε μεγάλο βαθμό αντιμετωπισθεί . Η επόμενη μεγάλη πρόκληση είναι η κατανόηση του πρωτεόματος, δηλαδή του συνόλου των πρωτεϊνών που εκφράζονται σε ένα κύτταρο. Εξαιρετικά σημαντικό βήμα προς την κατεύθυνση αυτή αποτελεί η μελέτη του δικτύου των πρωτεϊνικών αλληλεπιδράσεων. Οι πρωτεϊνικές αλληλεπιδράσεις αποτελούν ένα ιδιαίτερα σημαντικό πεδίο έρευνας καθώς ρυθμίζουν ένα τεράστιο αριθμό διεργασιών οι οποίες είναι βασικές για τη δομή και τη λειτουργία του. Εκτιμάται πως το δίκτυο των πρωτεϊνικών αλληλεπιδράσεων στον άνθρωπο αφορά περίπου 130,000 ζεύγη αλληλεπιδράσεων, ενώ ο αριθμός των αλληλεπιδράσεων που έχουν ταυτοποιηθεί αλλά παραμένει ως ζητούμενο η επιβεβαίωση των αντίστοιχων πειραματικών αποτελεσμάτων, αποτελεί μόνο το 8%, περίπου, του πραγματικού δικτύου. Ο κύριος όγκος πληροφορίας στο πεδίο αυτό δίνεται μέσα από βάσεις δεδομένων και έρχεται από μεγάλης κλίμακας πειράματα υψηλής απόδοσης τα οποία όμως, έχει βρεθεί πως δίνουν σε μεγάλο ποσοστό ανακριβή αποτελέσματα εξ αιτίας μιας σειράς εγγενών προβλημάτων των μεθόδων και της φύσεως των πρωτεϊνών. Η εκτίμηση του πραγματικού μεγέθους του δικτύου των πρωτεϊνικών αλληλεπιδράσεων υποδεικνύει και τον όγκο των δεδομένων που θα παραχθεί στο εγγύς μέλλον αλλά και την ανάγκη για βελτίωση της αξιοπιστίας της πληροφορίας που διατίθεται στις σχετικές βάσεις δεδομένων. Σκοπός αυτής της εργασίας είναι η ανάπτυξη μιας αναλυτικής βάσης δεδομένων γνώσης για την ταυτοποίηση δικτύων πρωτεϊνικών αλληλεπιδράσεων αντλώντας πληροφορία από επιλεγμένες μετά από αξιολόγηση, δημόσιες βάσεις πρωτεϊνικών αλληλεπιδράσεων. Η συλλογή αυτή της πληροφορίας θα οδηγήσει μεσοπρόθεσμα στη δημιουργία μιας βάσης δεδομένων για τη διαχείριση της συλλογής, της οργάνωσης και της ανάκτησης δεδομένων πρωτεϊνικών αλληλεπιδράσεων όπου κατάλληλα υπολογιστικά εργαλεία θα αναπτυχθούν ώστε να αξιολογηθεί ο βαθμός αξιοπιστίας της καταχωρημένης σχετικής πληροφορίας σε μια μεγάλη ομάδα δημόσιων γονιδιωματικών βάσεων δεδομένων. Επίσης θα υπάρξει η δυνατότητα χρήσης εργαλείων για την ανάλυση των αξιολογημένων δεδομένων πρωτεϊνικών αλληλεπιδράσεων, την μελέτη πρωτεϊνών με άγνωστη λειτουργία αλλά και τον προσδιορισμό μη καταγεγραμμένων έως τώρα πρωτεϊνικών συμπλεγμάτων. / The elucidation of protein-protein interaction (PPI) networks (protein interactomes) is a major objective of systems biology. This task is crucial for furthering our understanding of the cellular machinery dynamics, in light of the fundamental role of proteins in cellular function. The development of high-throughput methods for PPI identification, including the widely used yeast two hybrid and the mass spectrometry of co-immunoprecipitated complexes, drastically increased the PPI data in model organisms and the human. However, these methods suffer from intrinsic detection biases and >70% of false positives. Moreover, independent public databases (dbs) of experimentally derived PPIs exhibit a remarkably limited overlap, mainly due to uncoordinated data validation and curation criteria. These limitations scale up in highly complex systems like the human for which only 8-10% of the estimated PPIs have been determined. Furthermore, new PPI prediction is affected by the current data quality and quantity along with predictive algorithm limitations to incorporate the available protein information. Thus, there is initially a need for a systematic curation of multiple datasets into one common db. We have integrated high- and low- throughput experimental data, ortholog protein interactions, protein domain interactions, and protein structure/function and expression data from twelve highly informative and updated dbs into one local db using the Microsoft_SQL_Server. The db selection was based on their unique gene content, PPIs recorded, annotation depth, curation methodology and relational scheme. This data will be enriched with PPI information mined from the literature. The final dataset will be appropriately scored to rank and validate the PPIs with increased confidence, forming the basis for a human interactome knowledge base.

O feijão-comum (Phaseolus vulgaris) é atacado por uma gama de patógenos que afetam a produtividade das lavouras e a qualidade dos grãos. Dentre os patógenos de importância econômica para a cultura no Brasil, destaca-se o nematoide das galhas (Meloidogyne incognita). Embora haja relatos sobre a avaliação de cultivares na presença de M. incognita, as fontes de resistência tem se mostrado pouco efetivas. Por isso, pesquisas que possibilitem um melhor entendimento sobre a interação planta-nematoide são de extrema valia e devem nortear novas estratégias para o melhoramento do feijoeiro. Assim, no presente estudo, 18 cultivares de P. vulgaris foram avaliadas quanto à resistência a M. incognita raça 3, sendo que quatro comportaram-se como pouco suscetíveis, 11 como moderadamente suscetíveis e três altamente suscetíveis. A cultivar IPR Saracura mostrou menor grau de suscetibilidade e foi, então, usada na construção de 12 bibliotecas de RNAseq, visando à identificação dos genes envolvidos na reposta à infecção pelo nematoide. Foram adotados dois tratamentos, 4 e 10 DAI (dias após inoculação), compostos de plantas inoculadas e controles. Primeiramente, realizou-se o mapeamento dos transcritos de cada biblioteca, tomando como referência o genoma de P. vulgaris (G19833), o que resultou na identificação de 27.195 unigenes. Em seguida, foi realizada a quantificação da expressão dos transcritos mapeados e genes diferencialmente expressos foram identificados. No total, 191 genes do hospedeiro apresentaram expressão diferencial, considerando-se: i) o tratamento inoculado em relação ao controle; ii) a razão de expressão (Fold Change - FC) mínima absoluta igual a 4; iii) o nível de significância ? = 0,05. Do total, 120 genes foram identificados aos 4 DAI e 71 aos 10 DAI. As sequências mapeadas foram contrastadas àquelas dos bancos de dados NCBI e TAIR, usando a ferramenta BLASTx e, posteriormente, anotadas usando os softwares Blast2GO e MapMan. Detectou-se similaridade com genes codificadores de proteínas conhecidas para 90% (24.604/27.195) dos unigenes, sendo que 69% (16.991/24.604) deles foram anotados. Quanto à expressão diferencial, 98% (188/191) dos transcritos mostraram similaridade com proteínas conhecidas e 67% (127/188) puderam ser anotados. Os transcritos foram atribuídos a diferentes categorias funcionais putativas, predominando o termo ontológico \'processos metabólicos\', em ambas as plataformas. A anotação dos genes na plataforma MapMan mostrou abundância das categorias da via de resposta a estresse, com predominância de genes de defesa superexpressos aos 4 DAI e reprimidos aos 10 DAI. Por fim, 10 genes mostraram expressão diferencial tanto aos 4 como aos 10 DAI: sete deles foram estáveis, sendo superexpressos nas plantas inoculadas, e três apresentaram comportamentos opostos nos momentos avaliados. Ênfase foi dada a um gene que codifica uma \'probable inactive ADP-ribosyltransferase\' e a quatro genes de resposta a ferimento. / The common bean (Phaseolus vulgaris) is attacked by a range of pathogens, which affect crop yield and the quality of grains. Among the pathogens of economic significance to the crop in Brazil, the root-knot nematodes (Meloidogyne incognita) deserve attention. Though there are some reports on cultivar evaluation in presence of M. incognita, the resistance sources have not being effective. Therefore, it is of valuable importance research projects that could lead to a better understanding of plant-nematode interaction and to indicate new strategies for common bean breeding. In the present study, 18 cultivars of P. vulgaris were evaluated in regard to their resistance to M. incognita race 3; four were less susceptible, 11 moderately susceptible, and three were highly susceptible. \'IPR Saracura\' behaved as the less susceptible cultivar and then was selected for the construction of 12 RNAseq libraries, aiming at the identification of genes differentially expressed in response to nematode infection. Two treatments were adopted, 4 and 10 days after inoculation (DAI), each comprised of inoculated and control plants. Firstly, the transcripts were mapped to the reference genome of P. vulgaris (G19833), resulting in the identification of 27,195 unigenes. Then, the mapped transcript\'s expression was quantified and differentially expressed genes were identified. In total, 191 genes of the host plant showed differential expression taking into consideration: i) the inoculated treatments in relation to their control; ii) an absolute fold change (FC) >= 4; iii) a level of significance ? = 0,05. Of the total, 120 genes were detected at 4 DAI and 71 at 10 DAI. The mapped sequences were compared against those deposited in NCBI and TAIR databanks using BLASTx and subsequently annotated using Blast2GO and MapMan softwares. Similarity to known proteins was detected for 90% of the unigenes (24,604/27,195) and 69% (16,991/24,604) of them were annotated. Regarding assessing differential expression, 98% (188/191) of the transcripts showed similarity to known proteins and 67% (127/188) were annotated. Transcripts were attributed to different putative functional categories and the ontological term \'metabolic process\' was predominant within both platforms. Gene annotation within MapMan platform showed predominance of stress-related pathway categories, with prevalence of defense genes overexpressed at 4 DAI and repressed at 10 DAI. Finally, 10 genes showed differential expression at both 4 and 10 DAI: seven were stably overexpressed in the inoculated plants, and three showed an opposite behavior regarding the evaluation periods. Attention was given to a gene encoding a probable inactive ADP-ribosyltransferase and four genes related to wound response.

Orientador: Jorg Kobarg / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-25T15:15:29Z (GMT). No. of bitstreams: 1 Souza_EdmarciaElisa_D.pdf: 15682912 bytes, checksum: e58bfe67bbf5f3bc0979ec28db650292 (MD5) Previous issue date: 2014 / Resumo: As proteínas Neks (NIMA-related kinases) representam uma família de 11 quinases humanas nomeadas Nek1 a 11 que compartilham 40 a 45% de identidade de sequência com o regulador mitótico NIMA identificado em Aspergillus nidulans. O sinergismo entre os mecanismos que dirigem a mitose é essencial para a adequada divisão celular e sua desregulação é correlacionada ao aparecimento de cânceres humanos. As Neks são essenciais para progressão do ciclo celular e por isso têm recebido especial atenção como alvos para terapia do câncer. A Nek7 humana, por sua vez, contribui para formação do fuso mitótico e biogênese dos centrossomos. Neste trabalho, nós revelamos a Nek7 como uma quinase multifuncional. Nossos estudos demonstraram um amplo espectro de proteínas de interações com a Nek7 humana, classificadas dentro de múltiplas categorias funcionais, sobretudo, da divisão celular. Alguns novos parceiros de interação também são seus potencias substratos e, ainda, localizam com a Nek7 em estruturas essenciais para a mitose e citocinese. Nós evidenciamos ainda, que através de mecanismos distintos, os domínios N- e C-terminal de Nek6 e Nek7 podem contribuir diferencialmente para a regulação e catálise e podem proporcionar a base estrutural para a independência funcional dessas quinases na sinalização celular. Além disso, usando estudos baseados microscopia confocal e RNAi (RNA interference), nós mostramos que o interactor de Nek7, a proteína RGS2, é necessária para organização e orientação do fuso mitótico. Células em metáfase suprimidas de RGS2 apresentaram fenótipos tais como: prisão na mitose; defeitos na tensão dos cinetocóros e alinhamento dos cromossomos; desorganização do fuso mitótico; perturbação na redistribuição de proteínas do polo do fuso envolvidas em nucleação; mal-orientação do fuso mitótico; e redução de microtúbulos dos ásteres e de dinâmica. Além disso, tanto a supressão quanto a superexpressão das formas selvagem e quinase dead de Nek7 prejudicaram o recutamento de ?-tubulina para o polo do fuso. Esses achados introduz a participação de RGS2 na mitose e indicam que esta pode atuar cooperativamente com Nek7 para a precisa organização e formação do fuso mitótico. Por fim, empregando biologia de sistemas, nós mostramos um compreensivo interactoma das Neks, destacando para um possível crosstalking de todos os membros da família nos processos de regulação de centríolos e mitose; função ciliar e ciliopatias; e resposta a dano de DNA / Abstract: The Neks (NIMA-related kinases) proteins represent a human kinases family named Nek1 to 11 that share 40 to 45% of sequence identity with the established NIMA mitotic regulator, identified in Aspergillus nidulans. The synergism of the mechanisms that drive mitosis is essential for proper cell division and its dysregulation is correlated with the occurrence of human cancers. The Neks are essential for cell cycle progression and therefore have received attention as targets for cancer therapy and other diseases. Human Nek7 contributes to mitotic spindle formation and centrosome biogenesis. Herein, we reveal Nek7 as a multifunctional kinase. Our proteomic studies have demonstrated a broad spectrum of interaction proteins of human Nek7 classified into multiple functional categories, especially, cell division. Some new interaction partners are also potential Nek7 substrates and localize in key structure during mitosis and cytokinesis. We also evidenced that, through different mechanisms, the N- and C- terminal domains of Nek7 and Nek6 can differentially contribute to the regulation and catalysis and provide the basis for a functional independence of Nek6 and Nek7 in cell signaling. Furthermore, using studies based in confocal microscopy and RNAi we showed the Nek7 interactor, RGS2 protein, is required for organization and orientation of the mitotic spindle. Metaphase cells RGS2-depleted showed phenotypes such as: arrest in mitosis; defects in tension kinetochores and alignment chromosomes; disruption of the mitotic spindle; disturbance in the proteins redistribution of the spindle pole involved in nucleation and microtubule dynamics; mitotic spindle misorientation; and astral microtubules reduction. Furthermore, the suppression or both overexpression of Nek7 wild type or kinase dead impaired the recruitment of ?-tubulin to the spindle pole. These findings introduce the involvement of RGS2 in mitosis and indicate that it may act cooperatively with Nek7 for proper mitotic spindle organization and formation. Finally, employing systems biology, we showed a comprehensive Neks interactome, highlighting for a possible crosstalking of all family members in centrioles and mitosis regulation; ciliary and ciliopathies function; and response to DNA damage / Doutorado / Bioquimica / Doutora em Biologia Funcional e Molecular

Orientador: Jörg Kobarg / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-19T01:34:02Z (GMT). No. of bitstreams: 1 Santos_MarcosTadeudos_D.pdf: 15943486 bytes, checksum: 39810fdf0ace76e5e8963354bdc460ca (MD5) Previous issue date: 2011 / Resumo: O objetivo deste projeto foi estudar genes ativados em células do estroma da medula óssea, induzidos pela co-cultura com blastos leucêmicos, na tentativa de uma melhor compreensão sobre o crostalk entre estas células no microambiente tumoral. Nós identificamos Stanniocalcina-1 (STC1) como um potencial marcador molecular do microambiente tumoral, uma vez que sua expressão foi aumentada cerca de 7 vezes em células do estroma co-cultivadas com blastos leucêmicos primários. STC1 humana é uma glicoproteína secretada e tem sido descrita participando em diferentes processos fisiológicos, incluindo a angiogênese, hipóxia e principalmente, a carcinogênese. Nós produzimos a proteína recombinante STC1 no sistema baculovírus e também anticorpos monoclonais, usados em um ensaio ELISA, que agora será testado como um novo kit de diagnóstico de leucemia por uma empresa brasileira. Além disso, identificamos novos parceiros de interação para STC1 através do sistema de duplo hibrido em levedura sendo que algumas destas interações foram confirmadas por GST-pull down. A região Nterminal foi identificada como sendo a região responsável pela interação de STC1 com seus parceiros. Estudos de localização sub-celular por microscopia, revelaram uma deposição ubíqua citoplasmática e puntiforme nuclear, lembrando corpúsculos nucleares relacionados a SUMOilação. Embora STC1 interaja com a proteína SUMO1 e tenha uma predição de alta probabilidade para ser SUMOilada, ensaios in vitro e in vivo não conseguiram detectar STC1 SUMOilada. No entanto, observamos que STC1 regula a SUMOilação de forma significativa em três outras proteínas. Essas descobertas sugerem um novo papel para STC1 no ciclo de SUMOilação, agindo como uma SUMO E3 ligase. Observamos também que STC1 possui um receptor na membrana plasmática em linhagem de células leucêmicas K562 e que a incubação de STC1 com outras células leucêmicas parece favorecer a proliferação destas células ao passo que estimula uma maior produção da própria STC1 intracelular em células do estroma. Juntos, todos estes resultados abrem novas pistas promissoras a serem exploradas no futuro, uma vez que todos os resultados mostram ligações interessantes com estudos funcionais anteriores em STC1 / Abstract: The aims of this project is to study upregulated genes on bone marrow stromal cells, induced by the co-culture with leukemic blasts, trying to have a better understand about the crosstalk between these cells in the tumor microenvironment. We identified Stanniocalcin-1 (STC1) as a putative molecular marker for the leukemic microenvironment, once its expression was increased around 7 times in stromal cells co-cultivated with primary leukemic blasts. Human STC1 is a secreted glycoprotein that has been implicated in different physiological process, including angiogenesis, hypoxia and mainly in carcinogenesis. We produced the recombinant protein STC1 in baculovirus system and monoclonal antibodies for an ELISA assay that now will be tested as a new leukemia diagnostic kit by a Brazilian company. Moreover, we identified new interacting protein partners for STC1 by yeast two hybrid system and some of these interactions were confirmed by GST-pull down assays. The N-terminal region was mapped to be the region that mediates the interaction between STC1 and its partners. Microscopic subcellular localization, revealed an ubiquitous cytoplasmic and dot-like nuclear deposition, resembling SUMOylation related nuclear bodies. Although STC1 interacts with SUMO-1 and has a high theoretical prediction score for a SUMOylation site, in vitro and in vivo assays could not detect STC1 SUMOylation. However, we found that STC1 significantly regulates the SUMOylation of three other proteins. These ??ndings suggest a new role for STC1 in SUMOylation cycle, acting as a SUMO E3 ligase. We either observe that STC1 has a plasmatic membrane receptor in K562 leukemic cell lines and the incubation of STC1 with other leukemic cells suggest a increase of proliferation of these cells and stimulates the production of more intracellular STC1 at stromal cells. Together, all of these findings open promising new avenues to be explored in future detailed studies, since they all show interesting connections with previous functional studies on STC1 / Doutorado / Genetica Animal e Evolução / Doutor em Genetica e Biologia Molecular